Starting phenix.real_space_refine on Sun Oct 25 20:25:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q59_72223/10_2026/9q59_72223.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q59_72223/10_2026/9q59_72223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q59_72223/10_2026/9q59_72223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q59_72223/10_2026/9q59_72223.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q59_72223/10_2026/9q59_72223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q59_72223/10_2026/9q59_72223.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 92 5.16 5 C 11186 2.51 5 N 3166 2.21 5 O 3298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5971 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 721} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 5971 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 721} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2900 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 24, 'TRANS': 345} Chain breaks: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2900 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 24, 'TRANS': 345} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2031 SG CYS A 285 76.896 108.002 32.880 1.00 43.58 S ATOM 2156 SG CYS A 301 79.688 106.307 31.944 1.00 44.54 S ATOM 2655 SG CYS A 365 79.390 107.386 35.775 1.00 48.36 S ATOM 8002 SG CYS B 285 61.166 77.795 32.892 1.00 42.94 S ATOM 8127 SG CYS B 301 58.396 79.479 31.956 1.00 43.92 S ATOM 8626 SG CYS B 365 58.700 78.377 35.788 1.00 44.67 S Time building chain proxies: 4.42, per 1000 atoms: 0.25 Number of scatterers: 17744 At special positions: 0 Unit cell: (138.918, 186.594, 97.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 92 16.00 O 3298 8.00 N 3166 7.00 C 11186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 886.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 285 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 301 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 365 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 301 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 285 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 365 " 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 32 sheets defined 24.6% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.512A pdb=" N ARG A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 286 through 294 removed outlier: 3.818A pdb=" N TYR A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.509A pdb=" N ALA A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 523 through 537 removed outlier: 3.779A pdb=" N GLU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 549 removed outlier: 3.556A pdb=" N LEU A 549 " --> pdb=" O THR A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 558 through 566 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 639 through 650 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 748 through 750 No H-bonds generated for 'chain 'A' and resid 748 through 750' Processing helix chain 'B' and resid 85 through 93 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 226 through 231 removed outlier: 3.532A pdb=" N ARG B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.855A pdb=" N TYR B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 413 through 419 removed outlier: 3.522A pdb=" N ALA B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 481 through 485 Processing helix chain 'B' and resid 523 through 537 removed outlier: 3.755A pdb=" N GLU B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 549 removed outlier: 3.522A pdb=" N LEU B 549 " --> pdb=" O THR B 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 549' Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 618 through 631 Processing helix chain 'B' and resid 639 through 650 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 748 through 750 No H-bonds generated for 'chain 'B' and resid 748 through 750' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 440 through 451 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 481 through 485 removed outlier: 3.542A pdb=" N LYS C 484 " --> pdb=" O ASP C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 removed outlier: 3.821A pdb=" N MET C 529 " --> pdb=" O GLY C 525 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 536 " --> pdb=" O GLN C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 566 removed outlier: 3.544A pdb=" N VAL C 562 " --> pdb=" O LYS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 618 through 630 Processing helix chain 'C' and resid 639 through 650 Processing helix chain 'C' and resid 664 through 669 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 748 through 750 No H-bonds generated for 'chain 'C' and resid 748 through 750' Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 440 through 451 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'D' and resid 481 through 485 removed outlier: 3.545A pdb=" N LYS D 484 " --> pdb=" O ASP D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 537 removed outlier: 3.838A pdb=" N MET D 529 " --> pdb=" O GLY D 525 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 536 " --> pdb=" O GLN D 532 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 566 removed outlier: 3.606A pdb=" N VAL D 562 " --> pdb=" O LYS D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 618 through 630 Processing helix chain 'D' and resid 639 through 650 Processing helix chain 'D' and resid 664 through 669 Processing helix chain 'D' and resid 670 through 674 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 748 through 750 No H-bonds generated for 'chain 'D' and resid 748 through 750' Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 3.848A pdb=" N LYS B 766 " --> pdb=" O LYS B 760 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS B 716 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 725 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE B 724 " --> pdb=" O ASP B 746 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU B 742 " --> pdb=" O THR B 728 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ALA B 730 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE B 740 " --> pdb=" O ALA B 730 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP B 732 " --> pdb=" O LYS B 738 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS B 738 " --> pdb=" O TRP B 732 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN B 739 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY B 702 " --> pdb=" O THR B 773 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 37 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 192 removed outlier: 6.910A pdb=" N TYR A 349 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP A 273 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 351 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 268 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 189 through 192 removed outlier: 6.910A pdb=" N TYR A 349 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP A 273 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 351 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 197 through 202 Processing sheet with id=AA7, first strand: chain 'A' and resid 329 through 331 Processing sheet with id=AA8, first strand: chain 'A' and resid 424 through 426 Processing sheet with id=AA9, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB1, first strand: chain 'A' and resid 550 through 551 Processing sheet with id=AB2, first strand: chain 'A' and resid 490 through 496 removed outlier: 3.554A pdb=" N GLY A 506 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 504 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 22 removed outlier: 3.905A pdb=" N LYS A 766 " --> pdb=" O LYS A 760 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS A 716 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 725 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY A 725 " --> pdb=" O ASP A 746 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASP A 746 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE A 727 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ARG A 744 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 729 " --> pdb=" O LEU A 742 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 739 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY A 702 " --> pdb=" O THR A 773 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 37 Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 47 Processing sheet with id=AB6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.913A pdb=" N TYR B 349 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP B 273 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 351 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.913A pdb=" N TYR B 349 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP B 273 " --> pdb=" O TYR B 349 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 351 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 197 through 202 Processing sheet with id=AB9, first strand: chain 'B' and resid 329 through 331 Processing sheet with id=AC1, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC4, first strand: chain 'B' and resid 490 through 496 removed outlier: 3.584A pdb=" N GLY B 506 " --> pdb=" O SER B 493 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 504 " --> pdb=" O MET B 495 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 425 through 426 Processing sheet with id=AC6, first strand: chain 'C' and resid 567 through 569 Processing sheet with id=AC7, first strand: chain 'C' and resid 490 through 496 removed outlier: 3.577A pdb=" N ASP C 504 " --> pdb=" O MET C 495 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG C 515 " --> pdb=" O MET C 511 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 725 through 733 removed outlier: 7.806A pdb=" N GLY C 725 " --> pdb=" O ASP C 746 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASP C 746 " --> pdb=" O GLY C 725 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE C 727 " --> pdb=" O ARG C 744 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG C 744 " --> pdb=" O ILE C 727 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN C 739 " --> pdb=" O ILE C 705 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 702 " --> pdb=" O THR C 773 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AD1, first strand: chain 'D' and resid 424 through 426 Processing sheet with id=AD2, first strand: chain 'D' and resid 567 through 569 Processing sheet with id=AD3, first strand: chain 'D' and resid 490 through 496 removed outlier: 3.600A pdb=" N ASP D 504 " --> pdb=" O MET D 495 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG D 515 " --> pdb=" O MET D 511 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 725 through 733 removed outlier: 6.498A pdb=" N LEU D 742 " --> pdb=" O THR D 728 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA D 730 " --> pdb=" O ILE D 740 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 740 " --> pdb=" O ALA D 730 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP D 732 " --> pdb=" O LYS D 738 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LYS D 738 " --> pdb=" O TRP D 732 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN D 739 " --> pdb=" O ILE D 705 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY D 702 " --> pdb=" O THR D 773 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 718 through 719 717 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6052 1.34 - 1.46: 3885 1.46 - 1.58: 8117 1.58 - 1.70: 0 1.70 - 1.82: 152 Bond restraints: 18206 Sorted by residual: bond pdb=" N PHE C 775 " pdb=" CA PHE C 775 " ideal model delta sigma weight residual 1.462 1.496 -0.034 7.70e-03 1.69e+04 1.97e+01 bond pdb=" N PHE D 775 " pdb=" CA PHE D 775 " ideal model delta sigma weight residual 1.461 1.495 -0.034 9.20e-03 1.18e+04 1.38e+01 bond pdb=" N ILE C 772 " pdb=" CA ILE C 772 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.22e-02 6.72e+03 9.43e+00 bond pdb=" N ILE C 703 " pdb=" CA ILE C 703 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.14e-02 7.69e+03 8.84e+00 bond pdb=" N ILE D 703 " pdb=" CA ILE D 703 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.15e-02 7.56e+03 8.67e+00 ... (remaining 18201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 24113 1.69 - 3.37: 540 3.37 - 5.06: 74 5.06 - 6.74: 15 6.74 - 8.43: 2 Bond angle restraints: 24744 Sorted by residual: angle pdb=" CA PHE C 775 " pdb=" C PHE C 775 " pdb=" N PRO C 776 " ideal model delta sigma weight residual 120.52 124.36 -3.84 8.30e-01 1.45e+00 2.15e+01 angle pdb=" CA PHE D 775 " pdb=" CB PHE D 775 " pdb=" CG PHE D 775 " ideal model delta sigma weight residual 113.80 118.35 -4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" CA PHE C 775 " pdb=" CB PHE C 775 " pdb=" CG PHE C 775 " ideal model delta sigma weight residual 113.80 118.29 -4.49 1.00e+00 1.00e+00 2.02e+01 angle pdb=" C LEU A 761 " pdb=" CA LEU A 761 " pdb=" CB LEU A 761 " ideal model delta sigma weight residual 117.23 111.41 5.82 1.36e+00 5.41e-01 1.83e+01 angle pdb=" CA GLY D 702 " pdb=" C GLY D 702 " pdb=" O GLY D 702 " ideal model delta sigma weight residual 120.91 117.20 3.71 8.70e-01 1.32e+00 1.82e+01 ... (remaining 24739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9298 17.96 - 35.92: 1071 35.92 - 53.88: 370 53.88 - 71.84: 64 71.84 - 89.80: 15 Dihedral angle restraints: 10818 sinusoidal: 4324 harmonic: 6494 Sorted by residual: dihedral pdb=" N PHE C 775 " pdb=" C PHE C 775 " pdb=" CA PHE C 775 " pdb=" CB PHE C 775 " ideal model delta harmonic sigma weight residual 122.80 133.30 -10.50 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C PHE D 775 " pdb=" N PHE D 775 " pdb=" CA PHE D 775 " pdb=" CB PHE D 775 " ideal model delta harmonic sigma weight residual -122.60 -132.66 10.06 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" N PHE D 775 " pdb=" C PHE D 775 " pdb=" CA PHE D 775 " pdb=" CB PHE D 775 " ideal model delta harmonic sigma weight residual 122.80 132.83 -10.03 0 2.50e+00 1.60e-01 1.61e+01 ... (remaining 10815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2240 0.062 - 0.124: 353 0.124 - 0.186: 24 0.186 - 0.248: 5 0.248 - 0.310: 4 Chirality restraints: 2626 Sorted by residual: chirality pdb=" CA PHE C 775 " pdb=" N PHE C 775 " pdb=" C PHE C 775 " pdb=" CB PHE C 775 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA PHE D 775 " pdb=" N PHE D 775 " pdb=" C PHE D 775 " pdb=" CB PHE D 775 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA VAL C 701 " pdb=" N VAL C 701 " pdb=" C VAL C 701 " pdb=" CB VAL C 701 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 2623 not shown) Planarity restraints: 3296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 371 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C PRO A 371 " -0.048 2.00e-02 2.50e+03 pdb=" O PRO A 371 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA A 372 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 771 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C ARG D 771 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG D 771 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE D 772 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 497 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 498 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 498 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 498 " 0.028 5.00e-02 4.00e+02 ... (remaining 3293 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 8578 2.98 - 3.46: 16434 3.46 - 3.94: 31144 3.94 - 4.42: 36860 4.42 - 4.90: 60176 Nonbonded interactions: 153192 Sorted by model distance: nonbonded pdb=" OE2 GLU D 607 " pdb=" OH TYR D 778 " model vdw 2.500 3.040 nonbonded pdb=" OE2 GLU C 607 " pdb=" OH TYR C 778 " model vdw 2.514 3.040 nonbonded pdb=" O ASP D 423 " pdb=" OD1 ASP D 423 " model vdw 2.521 3.040 nonbonded pdb=" N ASN A 373 " pdb=" O ASN A 373 " model vdw 2.525 2.496 nonbonded pdb=" O ASP C 423 " pdb=" OD1 ASP C 423 " model vdw 2.537 3.040 ... (remaining 153187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.020 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 22.010 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18212 Z= 0.202 Angle : 0.590 8.428 24744 Z= 0.343 Chirality : 0.047 0.310 2626 Planarity : 0.005 0.050 3296 Dihedral : 17.418 89.803 6666 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.73 % Allowed : 26.28 % Favored : 70.98 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2280 helix: 0.22 (0.24), residues: 496 sheet: -0.02 (0.20), residues: 604 loop : -0.56 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 583 TYR 0.011 0.001 TYR B 445 PHE 0.012 0.001 PHE D 659 TRP 0.008 0.001 TRP D 431 HIS 0.006 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.20 (18206) covalent geometry : angle 0.58966 / 0.34 (24744) hydrogen bonds : bond 0.12361 / 8.46 ( 679) hydrogen bonds : angle 6.23106 / 4.34 ( 1974) metal coordination : bond 0.00189 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 0.689 Fit side-chains REVERT: A 45 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7800 (mm) REVERT: A 63 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7399 (ttm170) REVERT: A 203 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7945 (mpt180) REVERT: A 628 GLU cc_start: 0.8040 (mp0) cc_final: 0.7829 (mp0) REVERT: A 694 GLU cc_start: 0.7724 (tp30) cc_final: 0.7344 (tt0) REVERT: A 783 GLU cc_start: 0.7085 (pt0) cc_final: 0.6494 (pp20) REVERT: B 63 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7304 (ttm170) REVERT: B 332 ASP cc_start: 0.7872 (m-30) cc_final: 0.7580 (m-30) REVERT: B 628 GLU cc_start: 0.8038 (mp0) cc_final: 0.7598 (mm-30) REVERT: B 677 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6769 (ptpp) REVERT: B 726 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6817 (pm20) REVERT: B 783 GLU cc_start: 0.7159 (pt0) cc_final: 0.6756 (mt-10) REVERT: C 445 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7167 (t80) REVERT: C 447 SER cc_start: 0.8274 (m) cc_final: 0.7934 (p) REVERT: C 718 HIS cc_start: 0.6266 (m-70) cc_final: 0.6057 (m90) REVERT: D 445 TYR cc_start: 0.7997 (OUTLIER) cc_final: 0.7534 (t80) REVERT: D 708 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7093 (mtp180) outliers start: 50 outliers final: 26 residues processed: 283 average time/residue: 0.6425 time to fit residues: 202.3116 Evaluate side-chains 276 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 243 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain C residue 445 TYR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain D residue 445 TYR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 717 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 200] chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 373 ASN A 392 GLN A 450 ASN A 551 ASN B 450 ASN C 539 ASN C 662 GLN D 416 ASN D 539 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.121772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094548 restraints weight = 21548.595| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.42 r_work: 0.3007 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18212 Z= 0.147 Angle : 0.523 7.272 24744 Z= 0.272 Chirality : 0.045 0.231 2626 Planarity : 0.005 0.052 3296 Dihedral : 5.802 55.086 2568 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.83 % Allowed : 25.30 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2280 helix: 0.85 (0.24), residues: 496 sheet: 0.07 (0.20), residues: 596 loop : -0.56 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 583 TYR 0.012 0.001 TYR A 445 PHE 0.016 0.001 PHE C 659 TRP 0.008 0.001 TRP D 528 HIS 0.005 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (18206) covalent geometry : angle 0.52319 / 0.27 (24744) hydrogen bonds : bond 0.03617 / 2.54 ( 679) hydrogen bonds : angle 4.87757 / 3.39 ( 1974) metal coordination : bond 0.00434 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 251 time to evaluate : 0.604 Fit side-chains REVERT: A 63 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7635 (ttm170) REVERT: A 338 MET cc_start: 0.9080 (mmm) cc_final: 0.8817 (mmp) REVERT: A 515 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8050 (ttm170) REVERT: A 628 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: A 783 GLU cc_start: 0.7334 (pt0) cc_final: 0.6782 (pp20) REVERT: B 44 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8499 (tp) REVERT: B 63 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7556 (ttm170) REVERT: B 203 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8313 (mpt180) REVERT: B 534 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: B 783 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: C 583 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7143 (mtm180) REVERT: C 708 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7338 (mtp180) REVERT: C 718 HIS cc_start: 0.6291 (m-70) cc_final: 0.6033 (m90) REVERT: D 422 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7426 (mmt180) REVERT: D 583 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7026 (mtm180) outliers start: 70 outliers final: 32 residues processed: 296 average time/residue: 0.6287 time to fit residues: 207.1139 Evaluate side-chains 279 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 534 GLN Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 604 TYR Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [71, 183, 49, 23, 122, 7, 10, 77, 201, 48, 184] chunk 71 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 0.3980 chunk 77 optimal weight: 0.0870 chunk 201 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 392 GLN A 450 ASN A 539 ASN B 450 ASN B 539 ASN C 416 ASN C 539 ASN C 662 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.125003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.097870 restraints weight = 21527.472| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.45 r_work: 0.3031 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.0618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18212 Z= 0.094 Angle : 0.473 7.089 24744 Z= 0.243 Chirality : 0.043 0.183 2626 Planarity : 0.004 0.049 3296 Dihedral : 4.628 52.187 2524 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.55 % Allowed : 25.57 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2280 helix: 1.18 (0.24), residues: 496 sheet: 0.10 (0.20), residues: 598 loop : -0.50 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 583 TYR 0.015 0.001 TYR A 445 PHE 0.013 0.001 PHE C 659 TRP 0.010 0.001 TRP D 528 HIS 0.004 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.09 (18206) covalent geometry : angle 0.47311 / 0.24 (24744) hydrogen bonds : bond 0.02860 / 2.02 ( 679) hydrogen bonds : angle 4.52734 / 3.15 ( 1974) metal coordination : bond 0.00136 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 249 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7966 (mm) REVERT: A 63 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7505 (ttm170) REVERT: A 338 MET cc_start: 0.9024 (mmm) cc_final: 0.8736 (mmp) REVERT: A 515 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7959 (ttm170) REVERT: A 783 GLU cc_start: 0.7175 (pt0) cc_final: 0.6598 (pp20) REVERT: B 44 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8375 (tp) REVERT: B 63 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7445 (ttm170) REVERT: B 203 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8295 (mpt180) REVERT: B 726 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: B 783 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: C 583 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.6996 (mtm180) REVERT: C 718 HIS cc_start: 0.6112 (m-70) cc_final: 0.5860 (m90) outliers start: 65 outliers final: 28 residues processed: 290 average time/residue: 0.6230 time to fit residues: 201.6786 Evaluate side-chains 275 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 747 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [182, 220, 98, 97, 57, 214, 24, 54, 5, 189, 180] chunk 182 optimal weight: 0.2980 chunk 220 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 392 GLN A 450 ASN B 392 GLN B 450 ASN B 539 ASN C 539 ASN C 662 GLN D 534 GLN D 539 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.092960 restraints weight = 21431.871| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.41 r_work: 0.2973 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18212 Z= 0.182 Angle : 0.549 7.828 24744 Z= 0.285 Chirality : 0.046 0.185 2626 Planarity : 0.005 0.053 3296 Dihedral : 5.046 51.727 2524 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.19 % Allowed : 23.93 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2280 helix: 1.08 (0.24), residues: 496 sheet: 0.05 (0.20), residues: 608 loop : -0.54 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 583 TYR 0.014 0.001 TYR A 445 PHE 0.018 0.002 PHE C 659 TRP 0.008 0.001 TRP A 732 HIS 0.004 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (18206) covalent geometry : angle 0.54929 / 0.28 (24744) hydrogen bonds : bond 0.03441 / 2.43 ( 679) hydrogen bonds : angle 4.65540 / 3.24 ( 1974) metal coordination : bond 0.00535 / 0.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 252 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8012 (mm) REVERT: A 63 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7494 (ttm170) REVERT: A 338 MET cc_start: 0.9059 (mmm) cc_final: 0.8749 (mmp) REVERT: A 515 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8006 (ttm170) REVERT: A 783 GLU cc_start: 0.7205 (pt0) cc_final: 0.6619 (pp20) REVERT: B 44 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8432 (tp) REVERT: B 63 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7464 (ttm170) REVERT: B 203 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8248 (mpt180) REVERT: B 404 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8093 (mt-10) REVERT: B 534 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: B 628 GLU cc_start: 0.8126 (mp0) cc_final: 0.7896 (mp0) REVERT: B 726 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: B 783 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6883 (mt-10) REVERT: C 583 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.7011 (mtm180) REVERT: C 708 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7070 (mtp180) REVERT: D 422 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7401 (mmt180) REVERT: D 583 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.6984 (mtm180) outliers start: 95 outliers final: 45 residues processed: 309 average time/residue: 0.6289 time to fit residues: 216.2051 Evaluate side-chains 300 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 534 GLN Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 638 MET Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 773 THR Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 747 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [215, 3, 20, 30, 21, 145, 90, 42, 113, 17, 110] chunk 215 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 392 GLN A 450 ASN B 392 GLN B 450 ASN B 539 ASN C 534 GLN C 539 ASN D 534 GLN D 539 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.094371 restraints weight = 21435.085| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.41 r_work: 0.2994 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18212 Z= 0.131 Angle : 0.514 7.978 24744 Z= 0.266 Chirality : 0.044 0.179 2626 Planarity : 0.005 0.051 3296 Dihedral : 4.859 51.839 2520 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.37 % Allowed : 24.81 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2280 helix: 1.18 (0.24), residues: 496 sheet: 0.11 (0.20), residues: 608 loop : -0.59 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 583 TYR 0.016 0.001 TYR A 445 PHE 0.016 0.001 PHE C 659 TRP 0.009 0.001 TRP D 528 HIS 0.004 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (18206) covalent geometry : angle 0.51395 / 0.27 (24744) hydrogen bonds : bond 0.03109 / 2.20 ( 679) hydrogen bonds : angle 4.56161 / 3.18 ( 1974) metal coordination : bond 0.00310 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 247 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7459 (ttm170) REVERT: A 338 MET cc_start: 0.9054 (mmm) cc_final: 0.8741 (mmp) REVERT: A 515 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7950 (ttm170) REVERT: A 783 GLU cc_start: 0.7184 (pt0) cc_final: 0.6598 (pp20) REVERT: B 63 ARG cc_start: 0.7992 (ttp80) cc_final: 0.7446 (ttm170) REVERT: B 203 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8221 (mpt180) REVERT: B 404 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 726 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7025 (pm20) REVERT: B 783 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: C 583 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.6923 (mtm180) REVERT: C 708 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7054 (mtp180) REVERT: D 422 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7380 (mmt180) REVERT: D 583 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.6929 (mtm180) REVERT: D 638 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8436 (ttm) outliers start: 80 outliers final: 39 residues processed: 297 average time/residue: 0.6216 time to fit residues: 205.8606 Evaluate side-chains 286 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 86 HIS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 747 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [226, 201, 85, 152, 165, 166, 145, 116, 193, 56, 223] chunk 226 optimal weight: 9.9990 chunk 201 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 56 optimal weight: 0.0470 chunk 223 optimal weight: 0.0980 overall best weight: 1.6284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 392 GLN A 450 ASN B 392 GLN B 450 ASN B 539 ASN C 534 GLN C 539 ASN D 534 GLN D 539 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.120966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.093684 restraints weight = 21359.022| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.41 r_work: 0.2983 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18212 Z= 0.153 Angle : 0.530 8.195 24744 Z= 0.275 Chirality : 0.045 0.180 2626 Planarity : 0.005 0.052 3296 Dihedral : 4.907 51.515 2520 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.04 % Allowed : 25.25 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2280 helix: 1.13 (0.24), residues: 496 sheet: 0.09 (0.20), residues: 612 loop : -0.60 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 583 TYR 0.017 0.001 TYR A 445 PHE 0.020 0.001 PHE D 659 TRP 0.009 0.001 TRP D 732 HIS 0.003 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (18206) covalent geometry : angle 0.53007 / 0.27 (24744) hydrogen bonds : bond 0.03184 / 2.25 ( 679) hydrogen bonds : angle 4.55486 / 3.17 ( 1974) metal coordination : bond 0.00422 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 245 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7438 (ttm170) REVERT: A 338 MET cc_start: 0.9066 (mmm) cc_final: 0.8743 (mmp) REVERT: A 515 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7953 (ttm170) REVERT: A 783 GLU cc_start: 0.7160 (pt0) cc_final: 0.6572 (pp20) REVERT: B 63 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7420 (ttm170) REVERT: B 203 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8219 (mpt180) REVERT: B 404 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8085 (mt-10) REVERT: B 628 GLU cc_start: 0.8076 (mp0) cc_final: 0.7845 (mp0) REVERT: B 726 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: B 783 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: C 583 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.6914 (mtm180) REVERT: C 708 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7020 (mtp180) REVERT: D 422 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7351 (mmt180) REVERT: D 583 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.6924 (mtm180) REVERT: D 638 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8434 (ttm) outliers start: 74 outliers final: 48 residues processed: 290 average time/residue: 0.6427 time to fit residues: 207.5315 Evaluate side-chains 300 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 747 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [163, 210, 196, 55, 148, 134, 47, 138, 11, 150, 205] chunk 163 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 ASN A 86 HIS A 392 GLN A 450 ASN B 392 GLN B 450 ASN C 534 GLN C 539 ASN C 718 HIS D 534 GLN D 539 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.118218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.090573 restraints weight = 21617.323| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.45 r_work: 0.2893 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 18212 Z= 0.273 Angle : 0.625 8.633 24744 Z= 0.326 Chirality : 0.050 0.199 2626 Planarity : 0.005 0.056 3296 Dihedral : 5.346 50.746 2520 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.70 % Allowed : 24.70 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2280 helix: 0.92 (0.24), residues: 496 sheet: -0.01 (0.20), residues: 606 loop : -0.65 (0.17), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 583 TYR 0.013 0.002 TYR B 445 PHE 0.024 0.002 PHE D 659 TRP 0.011 0.002 TRP A 732 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.27 (18206) covalent geometry : angle 0.62518 / 0.33 (24744) hydrogen bonds : bond 0.03925 / 2.78 ( 679) hydrogen bonds : angle 4.81443 / 3.35 ( 1974) metal coordination : bond 0.00835 / 0.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 244 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7471 (ttm170) REVERT: A 338 MET cc_start: 0.9114 (mmm) cc_final: 0.8799 (mmp) REVERT: A 404 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 515 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8015 (ttm170) REVERT: A 783 GLU cc_start: 0.7183 (pt0) cc_final: 0.6583 (pp20) REVERT: B 63 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7470 (ttm170) REVERT: B 404 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 427 TYR cc_start: 0.8753 (t80) cc_final: 0.8551 (t80) REVERT: B 726 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7099 (pm20) REVERT: B 783 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6921 (mt-10) REVERT: C 583 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.7028 (mtm180) REVERT: C 708 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7006 (mtp180) REVERT: D 422 ARG cc_start: 0.7773 (mtm110) cc_final: 0.7404 (mmt180) REVERT: D 583 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.7047 (mtm180) REVERT: D 708 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6328 (mmt180) outliers start: 86 outliers final: 50 residues processed: 298 average time/residue: 0.6467 time to fit residues: 213.9784 Evaluate side-chains 295 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 484 LYS Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 678 THR Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 747 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [67, 168, 171, 101, 94, 47, 50, 88, 158, 147, 97] chunk 67 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 47 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 158 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 392 GLN A 450 ASN A 539 ASN B 392 GLN B 450 ASN B 539 ASN C 534 GLN C 539 ASN D 534 GLN D 539 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.094860 restraints weight = 21472.840| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.41 r_work: 0.3016 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18212 Z= 0.108 Angle : 0.505 8.387 24744 Z= 0.262 Chirality : 0.044 0.171 2626 Planarity : 0.005 0.049 3296 Dihedral : 4.866 51.628 2520 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.90 % Allowed : 26.23 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2280 helix: 1.14 (0.24), residues: 494 sheet: -0.02 (0.20), residues: 610 loop : -0.64 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 583 TYR 0.020 0.001 TYR A 445 PHE 0.015 0.001 PHE C 659 TRP 0.012 0.001 TRP C 528 HIS 0.007 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (18206) covalent geometry : angle 0.50457 / 0.26 (24744) hydrogen bonds : bond 0.02894 / 2.05 ( 679) hydrogen bonds : angle 4.52041 / 3.14 ( 1974) metal coordination : bond 0.00188 / 0.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7603 (ttm170) REVERT: A 515 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8020 (ttm170) REVERT: A 783 GLU cc_start: 0.7343 (pt0) cc_final: 0.6721 (pp20) REVERT: B 63 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7589 (ttm170) REVERT: B 203 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8295 (mpt180) REVERT: B 445 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8475 (t80) REVERT: B 628 GLU cc_start: 0.8192 (mp0) cc_final: 0.7796 (mp0) REVERT: B 726 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: B 783 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6930 (mt-10) REVERT: C 534 GLN cc_start: 0.7945 (pt0) cc_final: 0.7721 (mt0) REVERT: C 583 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.7078 (mtm180) REVERT: C 708 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7104 (mtp180) REVERT: D 422 ARG cc_start: 0.7670 (mtm110) cc_final: 0.7408 (mmt180) REVERT: D 583 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.6969 (mtm180) REVERT: D 638 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8431 (ttm) outliers start: 53 outliers final: 32 residues processed: 283 average time/residue: 0.6360 time to fit residues: 200.0640 Evaluate side-chains 283 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 747 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [186, 29, 22, 53, 194, 211, 77, 98, 62, 220, 27] chunk 186 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 chunk 98 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 392 GLN A 450 ASN B 392 GLN B 450 ASN B 539 ASN C 539 ASN D 534 GLN D 539 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.121641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.094458 restraints weight = 21442.903| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.41 r_work: 0.2994 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18212 Z= 0.129 Angle : 0.522 8.761 24744 Z= 0.267 Chirality : 0.045 0.216 2626 Planarity : 0.005 0.049 3296 Dihedral : 4.864 51.483 2520 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.28 % Allowed : 25.90 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.17), residues: 2280 helix: 1.18 (0.24), residues: 494 sheet: -0.04 (0.20), residues: 614 loop : -0.60 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 583 TYR 0.017 0.001 TYR B 445 PHE 0.016 0.001 PHE D 659 TRP 0.010 0.001 TRP D 732 HIS 0.006 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (18206) covalent geometry : angle 0.52171 / 0.27 (24744) hydrogen bonds : bond 0.02990 / 2.12 ( 679) hydrogen bonds : angle 4.49685 / 3.13 ( 1974) metal coordination : bond 0.00309 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 246 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7941 (mm) REVERT: A 63 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7430 (ttm170) REVERT: A 515 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7945 (ttm170) REVERT: A 783 GLU cc_start: 0.7216 (pt0) cc_final: 0.6552 (pp20) REVERT: B 63 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7422 (ttm170) REVERT: B 203 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8246 (mpt180) REVERT: B 404 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 445 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8539 (t80) REVERT: B 628 GLU cc_start: 0.8064 (mp0) cc_final: 0.7835 (mp0) REVERT: B 726 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: B 783 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6755 (mt-10) REVERT: C 534 GLN cc_start: 0.7907 (pt0) cc_final: 0.7637 (mt0) REVERT: C 583 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.6861 (mtm180) REVERT: C 708 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7005 (mtp180) REVERT: D 422 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7358 (mmt180) REVERT: D 583 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.6896 (mtm180) REVERT: D 638 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8425 (ttm) REVERT: D 708 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6992 (mmm160) outliers start: 60 outliers final: 33 residues processed: 285 average time/residue: 0.6481 time to fit residues: 205.0467 Evaluate side-chains 287 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 445 TYR Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 747 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [169, 225, 153, 100, 128, 196, 21, 134, 44, 175, 177] chunk 169 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 153 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 chunk 177 optimal weight: 0.7980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 392 GLN A 450 ASN A 539 ASN B 392 GLN B 450 ASN C 539 ASN D 534 GLN D 539 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.119915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.092505 restraints weight = 21477.022| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.41 r_work: 0.2931 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18212 Z= 0.196 Angle : 0.570 8.659 24744 Z= 0.293 Chirality : 0.047 0.185 2626 Planarity : 0.005 0.053 3296 Dihedral : 5.063 50.972 2520 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.84 % Allowed : 26.39 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2280 helix: 1.08 (0.24), residues: 494 sheet: -0.07 (0.20), residues: 614 loop : -0.64 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 583 TYR 0.017 0.001 TYR B 445 PHE 0.020 0.002 PHE D 659 TRP 0.013 0.001 TRP D 732 HIS 0.007 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (18206) covalent geometry : angle 0.56950 / 0.29 (24744) hydrogen bonds : bond 0.03385 / 2.40 ( 679) hydrogen bonds : angle 4.61646 / 3.21 ( 1974) metal coordination : bond 0.00538 / 0.32 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 242 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 63 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7421 (ttm170) REVERT: A 404 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8081 (mt-10) REVERT: A 515 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7976 (ttm170) REVERT: A 783 GLU cc_start: 0.7210 (pt0) cc_final: 0.6545 (pp20) REVERT: B 63 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7432 (ttm170) REVERT: B 404 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8092 (mt-10) REVERT: B 628 GLU cc_start: 0.8071 (mp0) cc_final: 0.7839 (mp0) REVERT: B 726 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7033 (pm20) REVERT: B 783 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: C 534 GLN cc_start: 0.7858 (pt0) cc_final: 0.7643 (mt0) REVERT: C 583 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.6930 (mtm180) REVERT: C 704 GLU cc_start: 0.7079 (tt0) cc_final: 0.6443 (tm-30) REVERT: C 708 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6995 (mtp180) REVERT: D 422 ARG cc_start: 0.7753 (mtm110) cc_final: 0.7392 (mmt180) REVERT: D 583 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.6933 (mtm180) REVERT: D 638 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8417 (ttm) REVERT: D 708 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7027 (mmm160) outliers start: 52 outliers final: 34 residues processed: 279 average time/residue: 0.6730 time to fit residues: 208.4874 Evaluate side-chains 281 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 551 ASN Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 203 ARG Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 356 THR Chi-restraints excluded: chain B residue 551 ASN Chi-restraints excluded: chain B residue 654 PHE Chi-restraints excluded: chain B residue 726 GLU Chi-restraints excluded: chain B residue 783 GLU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 583 ARG Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain C residue 674 VAL Chi-restraints excluded: chain C residue 708 ARG Chi-restraints excluded: chain C residue 729 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 439 SER Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 638 MET Chi-restraints excluded: chain D residue 654 PHE Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 708 ARG Chi-restraints excluded: chain D residue 747 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: [208, 37, 96, 8, 226, 121, 18, 171, 124, 33, 213] chunk 208 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 HIS A 392 GLN A 450 ASN A 539 ASN B 392 GLN B 450 ASN C 539 ASN D 534 GLN D 539 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.093304 restraints weight = 21413.701| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.42 r_work: 0.2903 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18212 Z= 0.184 Angle : 0.564 7.925 24744 Z= 0.291 Chirality : 0.046 0.184 2626 Planarity : 0.005 0.053 3296 Dihedral : 5.090 50.850 2520 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.73 % Allowed : 26.45 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2280 helix: 1.05 (0.24), residues: 494 sheet: -0.07 (0.20), residues: 614 loop : -0.65 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 583 TYR 0.017 0.001 TYR A 445 PHE 0.019 0.002 PHE D 659 TRP 0.015 0.001 TRP D 732 HIS 0.007 0.001 HIS C 718 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.18 (18206) covalent geometry : angle 0.56448 / 0.29 (24744) hydrogen bonds : bond 0.03380 / 2.39 ( 679) hydrogen bonds : angle 4.63056 / 3.22 ( 1974) metal coordination : bond 0.00516 / 0.31 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6297.85 seconds wall clock time: 107 minutes 46.24 seconds (6466.24 seconds total)